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- PDB-1zy7: Crystal structure of the catalytic domain of an adenosine deamina... -

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Basic information

Entry
Database: PDB / ID: 1zy7
TitleCrystal structure of the catalytic domain of an adenosine deaminase that acts on RNA (hADAR2) bound to inositol hexakisphosphate (IHP)
ComponentsRNA-specific adenosine deaminase B1, isoform DRADA2a
KeywordsHYDROLASE / alpha/beta deaminase motif / zinc coordination / ionsitol hexakisphosphate
Function / homology
Function and homology information


hypoglossal nerve morphogenesis / muscle tissue morphogenesis / facial nerve morphogenesis / spinal cord ventral commissure morphogenesis / C6 deamination of adenosine / Formation of editosomes by ADAR proteins / double-stranded RNA adenine deaminase / tRNA-specific adenosine deaminase activity / double-stranded RNA adenosine deaminase activity / negative regulation of protein kinase activity by regulation of protein phosphorylation ...hypoglossal nerve morphogenesis / muscle tissue morphogenesis / facial nerve morphogenesis / spinal cord ventral commissure morphogenesis / C6 deamination of adenosine / Formation of editosomes by ADAR proteins / double-stranded RNA adenine deaminase / tRNA-specific adenosine deaminase activity / double-stranded RNA adenosine deaminase activity / negative regulation of protein kinase activity by regulation of protein phosphorylation / base conversion or substitution editing / neuromuscular process controlling posture / adenosine to inosine editing / neuromuscular synaptic transmission / innervation / motor neuron apoptotic process / motor behavior / positive regulation of viral genome replication / RNA processing / negative regulation of cell migration / multicellular organism growth / mRNA processing / double-stranded RNA binding / defense response to virus / regulation of cell cycle / negative regulation of cell population proliferation / mRNA binding / innate immune response / synapse / nucleolus / RNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
ADAR2, first double-stranded RNA binding domain / ADAR2, second double-stranded RNA binding domain / Adenosine deaminase/editase / Adenosine-deaminase (editase) domain / Adenosine to inosine editase domain profile. / tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase) / Double-stranded RNA binding motif / Cytokine IL1/FGF / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Double-stranded RNA-specific editase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.7 Å
AuthorsMacbeth, M.R. / Schubert, H.L. / Vandemark, A.P. / Lingam, A.T. / Hill, C.P. / Bass, B.L.
CitationJournal: Science / Year: 2005
Title: Inositol hexakisphosphate is bound in the ADAR2 core and required for RNA editing.
Authors: Macbeth, M.R. / Schubert, H.L. / Vandemark, A.P. / Lingam, A.T. / Hill, C.P. / Bass, B.L.
History
DepositionJun 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 14, 2020Group: Derived calculations / Structure summary
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._chem_comp.pdbx_synonyms / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-specific adenosine deaminase B1, isoform DRADA2a
B: RNA-specific adenosine deaminase B1, isoform DRADA2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5587
Polymers90,0112
Non-polymers1,5475
Water12,052669
1
A: RNA-specific adenosine deaminase B1, isoform DRADA2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7313
Polymers45,0051
Non-polymers7252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA-specific adenosine deaminase B1, isoform DRADA2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8274
Polymers45,0051
Non-polymers8223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.205, 121.192, 127.331
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RNA-specific adenosine deaminase B1, isoform DRADA2a


Mass: 45005.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BCY123 / References: UniProt: P78563
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 669 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: Bis-Tris, ammonium sulfate, PEG 3350, glycerol, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 15, 2004
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 89796 / Num. obs: 82849 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2
Reflection shellResolution: 1.7→1.76 Å / % possible all: 62.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.959 / SU B: 1.291 / SU ML: 0.045 / σ(F): 0 / ESU R: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.206 4219 -5%
Rwork0.173 ---
all0.17461 89813 --
obs0.17461 82731 92.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2---0.27 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5803 0 79 669 6551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225991
X-RAY DIFFRACTIONr_angle_refined_deg1.481.9658110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.745734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.14222.913254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.553151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8761551
X-RAY DIFFRACTIONr_chiral_restr0.0980.2908
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024389
X-RAY DIFFRACTIONr_nbd_refined0.2080.22994
X-RAY DIFFRACTIONr_nbtor_refined0.3040.24182
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2540
X-RAY DIFFRACTIONr_metal_ion_refined0.0410.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.242
X-RAY DIFFRACTIONr_mcbond_it0.9431.53763
X-RAY DIFFRACTIONr_mcangle_it1.57325913
X-RAY DIFFRACTIONr_scbond_it2.40932486
X-RAY DIFFRACTIONr_scangle_it3.6514.52197
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 276 -
Rwork0.173 3900 -
obs-5537 62.5 %

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